'For how long were you at work' would be more correct in the most obvious context. 'How long were you at work' doesn't specify what 'long' refers to: was it the time at work, or your (horizontal) length, or even the size of your genitals? With the right qualification, the sentence is fine: it might imply (in the future) questioning something that happened in the past eg. a policeman making enquiries about a crime.
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Pete855217Jun 16 '13 at 10:29

Thanks, yes that is why I wrote the last sentence: How long were you at work yesterday. I cannot use present perfect here, at least from what I know.
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LianJun 16 '13 at 10:38

'How long were you at work yesterday' is still incorrect, unless you qualify what 'long' actually refers to: height, time etc. 'For...long' is the correct way to question time duration. (ps. I've ignored the perennial 'don't end a sentence with a preposition' problem here).
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Pete855217Jun 16 '13 at 10:43

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I have no difficulty with the question as phrased. In the absence of any other context that might imply physical length, I think that length of time would be implied by all but the extremely pedantic readers/listeners (and I am frequently called pedantic). I agree that, very strictly, it should be For how long ... but that is rarely used.
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TrevorDJun 16 '13 at 11:13

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Ask any native speaker and they would automatically understand your questions. All three are perfectly comprehensible, the mere idea that someone by asking: How long were you at work? could possibly infer a question on the size of someone's genitals, as suggested by Pete855217 is absurd.
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Mari-Lou AJun 16 '13 at 11:33

1 Answer
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How long were you at work yesterday?
How long were you at work on 25th May?

and similar expressions are asking about the total duration of your period at work on the respective day. The simple past is sufficient.

How long had you been at work yesterday, before you felt ill?
How long had you been at work on 25th May, before the robbery happened?

are asking about the duration of your period at work prior to the particular event happening. The past perfect is required because you are asking about a period before another event that was also in the past.